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Tried a clean install of Firefox and then started from the beginning. No messing up this time.

Yep, that's always the best thing to do. First backup your bookmarks and such with the Mozilla Backup Tool then uninstall and manually delete all the Firefox directories then install the new version and use the backup tool to put everything back.

If you're going to do that, wouldn't it be easier to simply copy the bookmarks.html file from your mozilla/firefox profile directory and then simply move back into the new profile directory after you re-install?